tsiR

tsiR implements analyses based on the Susceptible-Infected-Recovered (TSIR) model to infer transmission parameters from incidence time series and to forward-simulate mechanistic disease dynamics for infectious disease research.

Key Features:

• Implementation: Implemented in the R programming language.
• TSIR extension: Extends the Susceptible-Infected-Recovered (TSIR) model for time-series epidemiological analysis.
• Parameter inference from incidence data: Infers transmission parameters from incidence data, including estimation of contact seasonality.
• Forward simulation: Forward-simulates mechanistic models using inferred parameters to project disease dynamics.
• Aggregated fitting approaches: Aggregates various fitting features described in the literature for TSIR model fitting.
• Diagnostic tools: Provides diagnostic tools to assess TSIR model fit to data.

Scientific Applications:

• Parameter estimation: Estimating transmission parameters and contact seasonality from incidence time-series of infectious diseases.
• Projection and scenario analysis: Forward projection of disease dynamics via mechanistic simulations based on inferred parameters.
• Model validation: Assessing TSIR model fit and robustness using diagnostic tools.
• Application domain: Analysis of incidence data from fully-immunizing infectious diseases.

Methodology:

Implemented in R; builds upon the Susceptible-Infected-Recovered (TSIR) model; performs parameter inference from incidence data including estimation of contact seasonality; forward-simulates mechanistic models based on inferred parameters; includes diagnostic tools and aggregates fitting approaches described in the literature.